The specials are as follows:
Charge your buster to the second level. (Yellow)
Now, while holding that, hold up on the analog stick. Your character will do their special move.
Mega Man: Three hit Shoryuken.
Proto Man:Short-range, three hit plasma flamethrower. (Use against Shade Man when he does his Noise Crush for an interesting result)
Bass: A flip kick. Three hits, but has a tendency to push Bass into whoever he's using it on.
Duo:An uppercut. Press Jump to jump, then hit Attack to have him attack again.
Now, in the "Find Wily" section, the attacks all change. Duo gets an extra punch before his uppercut, Protoman's flamethrower lasts longer and Bass gets another flip kick. Mega Man, however, stays the same, but supposedly gets a new move.
Anyone ever see it?
EDIT:This is for the Anniversary Collection for the Gamecube. As far as I know it works the same on the other versions, but I've never played those.